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Major bug fix to AUC of Summary method #3

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Merged
stufield merged 1 commit into from
Jul 7, 2026
Merged

Major bug fix to AUC of Summary method #3

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16 changes: 7 additions & 9 deletions R/utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -54,25 +54,23 @@ get_cores <- function() {
restore_rng_kind <- getFromNamespace("restore_rng_kind", "withr")

#' Internal for calculating the AUC for all stability paths
#' using the trapezoidal rule. Must use `abs()` because decreasing.
#'
#' @param x A `stabpath_matrix` entry of a `stab_path` object.
#'
#' @param values A vector of values to iterate over,
#' typically `lambda_norm`.
#' typically `lambda_norm` (`lambda / max(lambda)`).
#'
#' @importFrom utils head tail
#' @noRd
calc_path_auc <- function(x, values) {
stopifnot(
"Must pass `x` as a `stability path matrix`." = is_stabpath_matrix(x)
)
sum_diffs <- head(values, -1L) + tail(values, -1L)
# flip matrix to perform row-wise operations column-wise
vapply(
data.frame(t(x)),
function(.x) as.double(diff(.x) %*% sum_diffs) / 2,
0.1
"`x` must be a `stability path matrix`." = is_stabpath_matrix(x)
)
auc_trapz <- function(x, y) {
sum(abs(diff(x)) * (head(y, -1L) + tail(y, -1L)) / 2)
}
apply(x, 1L, auc_trapz, x = values)
}

log_rfu <- function(x) {
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48 changes: 24 additions & 24 deletions tests/testthat/_snaps/stability-selection.md
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Original file line number Diff line number Diff line change
Expand Up @@ -91,26 +91,26 @@
# A tibble: 20 x 4
feature MaxSelectProb AUC FDRbound
<chr> <dbl> <dbl> <dbl>
1 feat_t 0.93 0.404939 NA
2 feat_d 0.91 0.360777 NA
3 feat_q 0.905 0.308470 NA
4 feat_a 0.9 0.307907 NA
5 feat_g 0.895 0.273354 NA
6 feat_j 0.89 0.416035 NA
7 feat_s 0.89 0.322614 NA
8 feat_r 0.885 0.342585 NA
9 feat_m 0.88 0.408485 NA
10 feat_n 0.87 0.270069 NA
11 feat_b 0.865 0.290262 NA
12 feat_e 0.865 0.277968 NA
13 feat_c 0.85 0.335890 NA
14 feat_f 0.85 0.257492 NA
15 feat_h 0.845 0.291972 NA
16 feat_l 0.845 0.259685 NA
17 feat_o 0.825 0.250749 NA
18 feat_p 0.815 0.223145 NA
19 feat_k 0.81 0.257189 NA
20 feat_i 0.8 0.270370 NA
1 feat_t 0.93 0.436532 NA
2 feat_d 0.91 0.408626 NA
3 feat_q 0.905 0.256633 NA
4 feat_a 0.9 0.286384 NA
5 feat_g 0.895 0.222145 NA
6 feat_j 0.89 0.440141 NA
7 feat_s 0.89 0.291720 NA
8 feat_r 0.885 0.342005 NA
9 feat_m 0.88 0.533218 NA
10 feat_n 0.87 0.220431 NA
11 feat_b 0.865 0.245937 NA
12 feat_e 0.865 0.253644 NA
13 feat_c 0.85 0.287507 NA
14 feat_f 0.85 0.224109 NA
15 feat_h 0.845 0.243903 NA
16 feat_l 0.845 0.221616 NA
17 feat_o 0.825 0.198936 NA
18 feat_p 0.815 0.186961 NA
19 feat_k 0.81 0.216318 NA
20 feat_i 0.8 0.235128 NA

---

Expand All @@ -120,10 +120,10 @@
# A tibble: 4 x 4
feature MaxSelectProb AUC FDRbound
<chr> <dbl> <dbl> <dbl>
1 feat_t 0.93 0.404939 0.003125
2 feat_d 0.91 0.360777 0.00625
3 feat_q 0.905 0.308470 0.009375
4 feat_a 0.9 0.307907 0.0125
1 feat_t 0.93 0.436532 0.003125
2 feat_d 0.91 0.408626 0.00625
3 feat_q 0.905 0.256633 0.009375
4 feat_a 0.9 0.286384 0.0125

# `stab_sel` S3 print method returns expected known output

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